Starting phenix.real_space_refine on Mon Mar 25 08:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fld_29275/03_2024/8fld_29275_neut_updated.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.047 sd= 0.194 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 3718 5.49 5 Mg 87 5.21 5 S 284 5.16 5 C 79014 2.51 5 N 27908 2.21 5 O 37552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L7 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ASP 112": "OD1" <-> "OD2" Residue "LK PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NL PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148569 Number of models: 1 Model: "" Number of chains: 68 Chain: "BE" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1295 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 1 Chain: "L1" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3278 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 3, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 25, 'rna3p': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "L2" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1535 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 24, 'rna3p_pyr': 32} Link IDs: {'rna2p': 16, 'rna3p': 55} Chain breaks: 4 Chain: "L3" Number of atoms: 72381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3372, 72381 Classifications: {'RNA': 3372} Modifications used: {'rna2p': 6, 'rna2p_pur': 324, 'rna2p_pyr': 210, 'rna3p': 82, 'rna3p_pur': 1492, 'rna3p_pyr': 1240} Link IDs: {'rna2p': 539, 'rna3p': 2832} Chain breaks: 31 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 33 Chain: "L4" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 54} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L5" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1349 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "L6" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "L7" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 191} Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LA" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LB" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1512 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LD" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1289 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "LE" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1264 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "LF" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 842 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "LG" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1034 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "LH" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1156 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LJ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "LK" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "LL" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LM" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 775 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Chain: "LN" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3239 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 386} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "LO" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "LP" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 879 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "LQ" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "LR" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 888 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "LV" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "LW" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "LX" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "LY" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "LZ" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NL" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2666 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 2 Chain: "NP" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain breaks: 1 Chain: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SB" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2376 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "SC" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 202} Chain breaks: 2 Chain: "SD" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "SE" Number of atoms: 1869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 bond proxies already assigned to first conformer: 1883 Chain: "SF" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 230} Chain: "SG" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "SH" Number of atoms: 1275 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} bond proxies already assigned to first conformer: 1289 Chain: "SI" Number of atoms: 1937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1950 Chain: "SK" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1721 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "SL" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1917 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "SM" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3278 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 380} Chain breaks: 2 Chain: "SQ" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 610 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 573 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "SR" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2002 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 232} Chain breaks: 2 Chain: "SV" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1184 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L1" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L3" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Unusual residues: {' MG': 72} Classifications: {'undetermined': 72} Link IDs: {None: 71} Chain: "L4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "LG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A07K6 SG CYSLR 46 86.808 183.240 122.557 1.00 51.15 S ATOM A07KN SG CYSLR 49 85.673 186.489 124.149 1.00 56.62 S ATOM A07RY SG CYSLR 83 83.518 185.094 121.406 1.00 45.25 S ATOM A07SI SG CYSLR 86 87.011 186.161 120.480 1.00 48.08 S ATOM A0A4U SG CYSLV 12 189.817 116.134 157.701 1.00 32.47 S ATOM A0A5I SG CYSLV 15 193.006 115.088 156.155 1.00 34.59 S ATOM A0AIJ SG CYSLV 72 192.082 118.958 156.512 1.00 35.61 S ATOM A0AJK SG CYSLV 77 190.310 116.544 154.084 1.00 42.55 S ATOM A0ATU SG CYSLW 19 95.184 128.091 141.918 1.00 33.48 S ATOM A0AUM SG CYSLW 22 95.775 125.332 144.448 1.00 32.62 S ATOM A0AX5 SG CYSLW 34 97.751 128.545 144.634 1.00 28.76 S ATOM A0AXO SG CYSLW 37 98.509 126.161 141.885 1.00 31.67 S ATOM A0BHV SG CYSLX 39 97.639 194.545 130.805 1.00 49.71 S ATOM A0BII SG CYSLX 42 94.236 196.144 130.690 1.00 49.41 S ATOM A0BLW SG CYSLX 57 94.703 193.131 132.767 1.00 48.34 S ATOM A0BMC SG CYSLX 60 94.870 192.685 129.022 1.00 49.59 S ATOM A0FEA SG CYSNP 63 76.431 201.632 201.424 1.00 59.11 S ATOM A0FET SG CYSNP 66 74.443 198.339 201.501 1.00 58.33 S ATOM A10J3 SG CYSSV 6 65.200 182.787 221.629 1.00 47.07 S ATOM A10JW SG CYSSV 9 61.590 181.491 221.395 1.00 45.45 S ATOM A10P0 SG CYSSV 32 64.213 179.105 222.410 1.00 44.67 S ATOM A10PU SG CYSSV 36 64.204 180.249 218.901 1.00 43.16 S Time building chain proxies: 58.15, per 1000 atoms: 0.39 Number of scatterers: 148569 At special positions: 0 Unit cell: (258.352, 243.344, 323.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 284 16.00 P 3718 15.00 Mg 87 11.99 O 37552 8.00 N 27908 7.00 C 79014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 56.82 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 202 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 46 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 83 " pdb=" ZNLV 200 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 77 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 12 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 15 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb=" ZNLW 101 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 19 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb=" ZNNP 500 " pdb="ZN ZNNP 500 " - pdb=" ND1 HISNP 85 " pdb="ZN ZNNP 500 " - pdb=" NE2 HISNP 79 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 63 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 66 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 32 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15968 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 315 helices and 76 sheets defined 45.6% alpha, 12.1% beta 1160 base pairs and 1839 stacking pairs defined. Time for finding SS restraints: 77.95 Creating SS restraints... Processing helix chain 'BE' and resid 42 through 47 removed outlier: 4.175A pdb=" N PHEBE 46 " --> pdb=" O LYSBE 42 " (cutoff:3.500A) Proline residue: BE 47 - end of helix No H-bonds generated for 'chain 'BE' and resid 42 through 47' Processing helix chain 'BE' and resid 61 through 80 Processing helix chain 'BE' and resid 144 through 160 removed outlier: 3.632A pdb=" N PHEBE 157 " --> pdb=" O ARGBE 153 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYSBE 158 " --> pdb=" O ARGBE 154 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHEBE 159 " --> pdb=" O ALABE 155 " (cutoff:3.500A) Proline residue: BE 160 - end of helix Processing helix chain 'BE' and resid 178 through 188 removed outlier: 4.035A pdb=" N GLUBE 182 " --> pdb=" O ALABE 178 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASPBE 183 " --> pdb=" O ASPBE 179 " (cutoff:3.500A) Processing helix chain 'BE' and resid 205 through 214 removed outlier: 4.223A pdb=" N TRPBE 209 " --> pdb=" O PROBE 205 " (cutoff:3.500A) Processing helix chain 'L5' and resid 30 through 44 Processing helix chain 'L5' and resid 76 through 91 removed outlier: 4.214A pdb=" N GLUL5 80 " --> pdb=" O GLYL5 76 " (cutoff:3.500A) Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.113A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLYL5 116 " --> pdb=" O HISL5 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L5' and resid 111 through 116' Processing helix chain 'L5' and resid 140 through 145 removed outlier: 6.243A pdb=" N LYSL5 145 " --> pdb=" O ILEL5 141 " (cutoff:3.500A) Processing helix chain 'L5' and resid 152 through 157 removed outlier: 5.993A pdb=" N ILEL5 157 " --> pdb=" O ALAL5 153 " (cutoff:3.500A) Processing helix chain 'L5' and resid 158 through 170 Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.280A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VALL6 22 " --> pdb=" O TRPL6 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 17 through 22' Processing helix chain 'L6' and resid 27 through 47 Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.131A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.524A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L6' and resid 140 through 147 removed outlier: 3.568A pdb=" N LEUL6 146 " --> pdb=" O GLUL6 142 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 176 Processing helix chain 'L6' and resid 177 through 192 Processing helix chain 'L6' and resid 193 through 211 removed outlier: 3.560A pdb=" N LYSL6 209 " --> pdb=" O GLNL6 205 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.547A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 60 removed outlier: 3.991A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.828A pdb=" N GLYL7 69 " --> pdb=" O ASNL7 65 " (cutoff:3.500A) Proline residue: L7 70 - end of helix No H-bonds generated for 'chain 'L7' and resid 65 through 70' Processing helix chain 'L7' and resid 75 through 89 removed outlier: 3.542A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.731A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.937A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 151 through 190 removed outlier: 5.404A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.525A pdb=" N VALL7 195 " --> pdb=" O LYSL7 191 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.836A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 removed outlier: 3.621A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.658A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.870A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.557A pdb=" N GLUL8 126 " --> pdb=" O ILEL8 122 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 4.000A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.756A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SERL9 34 " --> pdb=" O TYRL9 30 " (cutoff:3.500A) Processing helix chain 'L9' and resid 44 through 52 Processing helix chain 'L9' and resid 83 through 88 removed outlier: 3.949A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLYL9 88 " --> pdb=" O PROL9 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 83 through 88' Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.668A pdb=" N HISL9 109 " --> pdb=" O ARGL9 105 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.721A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 147 through 153 removed outlier: 6.154A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.612A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 10 through 15 removed outlier: 3.783A pdb=" N SERLA 14 " --> pdb=" O ASNLA 10 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N CYSLA 15 " --> pdb=" O PROLA 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 10 through 15' Processing helix chain 'LA' and resid 25 through 37 removed outlier: 3.515A pdb=" N ALALA 35 " --> pdb=" O GLULA 31 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 removed outlier: 3.504A pdb=" N LEULA 53 " --> pdb=" O LYSLA 49 " (cutoff:3.500A) Processing helix chain 'LA' and resid 72 through 77 removed outlier: 4.897A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 72 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.169A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.594A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.662A pdb=" N ALALB 116 " --> pdb=" O ARGLB 112 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.429A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) Processing helix chain 'LB' and resid 7 through 12 removed outlier: 4.697A pdb=" N ARGLB 11 " --> pdb=" O ASNLB 8 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYSLB 12 " --> pdb=" O LYSLB 9 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.887A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.877A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.937A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LD' and resid 4 through 16 Processing helix chain 'LD' and resid 18 through 23 removed outlier: 3.658A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TRPLD 23 " --> pdb=" O LYSLD 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 18 through 23' Processing helix chain 'LD' and resid 28 through 36 removed outlier: 3.577A pdb=" N ASNLD 34 " --> pdb=" O ASNLD 30 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASNLD 36 " --> pdb=" O ILELD 32 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 removed outlier: 3.607A pdb=" N LYSLD 43 " --> pdb=" O GLNLD 39 " (cutoff:3.500A) Processing helix chain 'LD' and resid 60 through 73 removed outlier: 3.519A pdb=" N LYSLD 72 " --> pdb=" O LEULD 68 " (cutoff:3.500A) Processing helix chain 'LD' and resid 77 through 82 removed outlier: 5.967A pdb=" N LYSLD 82 " --> pdb=" O ILELD 78 " (cutoff:3.500A) Processing helix chain 'LD' and resid 84 through 113 Proline residue: LD 90 - end of helix removed outlier: 6.574A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 3.520A pdb=" N LYSLD 126 " --> pdb=" O SERLD 122 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 Processing helix chain 'LE' and resid 11 through 16 removed outlier: 4.443A pdb=" N PHELE 15 " --> pdb=" O THRLE 11 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SERLE 16 " --> pdb=" O ARGLE 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 11 through 16' Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.553A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N METLE 31 " --> pdb=" O LEULE 27 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 26 through 32' Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.588A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLYLE 59 " --> pdb=" O LYSLE 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 54 through 59' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 4.076A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 99 through 121 removed outlier: 3.570A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 Processing helix chain 'LF' and resid 55 through 60 Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.888A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.645A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYSLG 74 " --> pdb=" O PROLG 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 69 through 74' Processing helix chain 'LG' and resid 122 through 130 removed outlier: 3.518A pdb=" N LEULG 128 " --> pdb=" O GLULG 124 " (cutoff:3.500A) Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 4.042A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.606A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 removed outlier: 3.511A pdb=" N LYSLH 89 " --> pdb=" O SERLH 85 " (cutoff:3.500A) Processing helix chain 'LH' and resid 105 through 117 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.820A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SERLI 31 " --> pdb=" O ARGLI 27 " (cutoff:3.500A) Processing helix chain 'LI' and resid 35 through 43 removed outlier: 3.503A pdb=" N GLNLI 40 " --> pdb=" O LYSLI 36 " (cutoff:3.500A) Processing helix chain 'LI' and resid 100 through 105 removed outlier: 4.095A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 removed outlier: 3.879A pdb=" N LEULI 119 " --> pdb=" O ARGLI 115 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLULI 120 " --> pdb=" O LYSLI 116 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 4.035A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.729A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N METLJ 81 " --> pdb=" O TYRLJ 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 76 through 81' Processing helix chain 'LJ' and resid 92 through 97 removed outlier: 4.157A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 removed outlier: 4.767A pdb=" N ARGLJ 102 " --> pdb=" O LYSLJ 98 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASPLJ 103 " --> pdb=" O ASPLJ 99 " (cutoff:3.500A) Proline residue: LJ 104 - end of helix No H-bonds generated for 'chain 'LJ' and resid 98 through 104' Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.654A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.682A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 7 removed outlier: 3.976A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYSLK 7 " --> pdb=" O SERLK 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 2 through 7' Processing helix chain 'LK' and resid 41 through 48 Processing helix chain 'LK' and resid 64 through 69 removed outlier: 4.252A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHELK 69 " --> pdb=" O ARGLK 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 64 through 69' Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.377A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.857A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.545A pdb=" N VALLK 140 " --> pdb=" O LYSLK 136 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLYLK 141 " --> pdb=" O ILELK 137 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 5.896A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.516A pdb=" N ILELL 97 " --> pdb=" O ILELL 93 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.521A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYSLL 122 " --> pdb=" O LEULL 118 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 36 through 55 removed outlier: 3.650A pdb=" N ASNLM 50 " --> pdb=" O ALALM 46 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEULM 54 " --> pdb=" O ASNLM 50 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYSLM 55 " --> pdb=" O LYSLM 51 " (cutoff:3.500A) Processing helix chain 'LM' and resid 56 through 66 Processing helix chain 'LM' and resid 91 through 102 Proline residue: LM 102 - end of helix Processing helix chain 'LM' and resid 105 through 118 removed outlier: 3.647A pdb=" N ALALM 110 " --> pdb=" O LYSLM 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGLM 111 " --> pdb=" O ARGLM 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILELM 112 " --> pdb=" O ALALM 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARGLM 117 " --> pdb=" O ALALM 113 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.619A pdb=" N LEULN 17 " --> pdb=" O SERLN 13 " (cutoff:3.500A) Proline residue: LN 18 - end of helix No H-bonds generated for 'chain 'LN' and resid 13 through 18' Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.047A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.574A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 removed outlier: 3.553A pdb=" N CYSLN 157 " --> pdb=" O METLN 153 " (cutoff:3.500A) Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.136A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 removed outlier: 3.743A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEULN 201 " --> pdb=" O ALALN 197 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.967A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.837A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLULN 361 " --> pdb=" O ARGLN 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 356 through 361' Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LN' and resid 230 through 236 removed outlier: 4.241A pdb=" N TRPLN 235 " --> pdb=" O GLYLN 230 " (cutoff:3.500A) Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.611A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 removed outlier: 3.562A pdb=" N LYSLO 36 " --> pdb=" O LYSLO 32 " (cutoff:3.500A) Processing helix chain 'LO' and resid 53 through 68 Processing helix chain 'LO' and resid 77 through 86 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.791A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 58 removed outlier: 3.556A pdb=" N LEULP 46 " --> pdb=" O ALALP 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYSLP 47 " --> pdb=" O PROLP 43 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLYLP 58 " --> pdb=" O METLP 54 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.638A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 removed outlier: 3.640A pdb=" N ARGLQ 47 " --> pdb=" O ASNLQ 43 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 4.041A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.580A pdb=" N LYSLQ 109 " --> pdb=" O SERLQ 105 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.574A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SERLR 68 " --> pdb=" O LEULR 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 60 through 68' Processing helix chain 'LR' and resid 83 through 113 Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.986A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.598A pdb=" N LYSLS 46 " --> pdb=" O SERLS 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 94 removed outlier: 3.565A pdb=" N ARGLS 93 " --> pdb=" O ARGLS 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.762A pdb=" N LEULS 102 " --> pdb=" O HISLS 98 " (cutoff:3.500A) Processing helix chain 'LS' and resid 104 through 114 Processing helix chain 'LT' and resid 35 through 40 removed outlier: 4.004A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLULT 40 " --> pdb=" O ARGLT 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 35 through 40' Processing helix chain 'LU' and resid 25 through 30 removed outlier: 4.154A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 Processing helix chain 'LU' and resid 51 through 64 removed outlier: 3.594A pdb=" N VALLU 63 " --> pdb=" O GLULU 59 " (cutoff:3.500A) Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LV' and resid 35 through 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.960A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.606A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.193A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARGLW 72 " --> pdb=" O LYSLW 68 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 19 through 35 removed outlier: 4.254A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HISLX 34 " --> pdb=" O GLULX 30 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 removed outlier: 3.528A pdb=" N GLULX 88 " --> pdb=" O ARGLX 84 " (cutoff:3.500A) Processing helix chain 'LY' and resid 7 through 17 Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.554A pdb=" N ALALY 53 " --> pdb=" O ASPLY 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 3.660A pdb=" N LYSLZ 15 " --> pdb=" O ARGLZ 11 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 26 through 31 removed outlier: 4.282A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THRLZ 31 " --> pdb=" O ILELZ 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 26 through 31' Processing helix chain 'NK' and resid 12 through 33 removed outlier: 3.548A pdb=" N LYSNK 20 " --> pdb=" O GLUNK 16 " (cutoff:3.500A) Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 removed outlier: 3.610A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARGNK 109 " --> pdb=" O LEUNK 105 " (cutoff:3.500A) Processing helix chain 'NL' and resid 116 through 123 removed outlier: 3.512A pdb=" N GLUNL 123 " --> pdb=" O ASPNL 119 " (cutoff:3.500A) Processing helix chain 'NL' and resid 133 through 138 removed outlier: 3.888A pdb=" N HISNL 137 " --> pdb=" O ASPNL 133 " (cutoff:3.500A) Processing helix chain 'NL' and resid 141 through 159 Processing helix chain 'NL' and resid 162 through 173 Processing helix chain 'NL' and resid 185 through 190 removed outlier: 3.592A pdb=" N ARGNL 190 " --> pdb=" O ASPNL 186 " (cutoff:3.500A) Processing helix chain 'NL' and resid 200 through 205 Proline residue: NL 205 - end of helix Processing helix chain 'NL' and resid 210 through 218 Processing helix chain 'NL' and resid 225 through 230 removed outlier: 4.039A pdb=" N HISNL 229 " --> pdb=" O PRONL 225 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THRNL 230 " --> pdb=" O ALANL 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'NL' and resid 225 through 230' Processing helix chain 'NL' and resid 252 through 280 Processing helix chain 'NL' and resid 289 through 299 removed outlier: 3.503A pdb=" N PHENL 294 " --> pdb=" O GLNNL 290 " (cutoff:3.500A) Processing helix chain 'NL' and resid 338 through 371 removed outlier: 3.821A pdb=" N LEUNL 368 " --> pdb=" O ARGNL 364 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHENL 369 " --> pdb=" O HISNL 365 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARGNL 370 " --> pdb=" O GLNNL 366 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEUNL 371 " --> pdb=" O GLUNL 367 " (cutoff:3.500A) Processing helix chain 'NL' and resid 372 through 400 Processing helix chain 'NL' and resid 436 through 449 removed outlier: 3.567A pdb=" N GLNNL 446 " --> pdb=" O PHENL 442 " (cutoff:3.500A) Processing helix chain 'NL' and resid 470 through 477 removed outlier: 3.757A pdb=" N ILENL 476 " --> pdb=" O ALANL 472 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLNNL 477 " --> pdb=" O PHENL 473 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 20 removed outlier: 4.717A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYSNP 20 " --> pdb=" O ALANP 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'NP' and resid 15 through 20' Processing helix chain 'NP' and resid 27 through 36 removed outlier: 3.570A pdb=" N HISNP 32 " --> pdb=" O LEUNP 28 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLUNP 34 " --> pdb=" O GLUNP 30 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 82 removed outlier: 3.896A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) Processing helix chain 'NP' and resid 83 through 94 removed outlier: 3.552A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.625A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.610A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.917A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.713A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.680A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.224A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 removed outlier: 3.622A pdb=" N LEUSA 170 " --> pdb=" O GLUSA 166 " (cutoff:3.500A) Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.879A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.650A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 263 removed outlier: 3.532A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.850A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.576A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.667A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 16 Processing helix chain 'SB' and resid 20 through 26 Processing helix chain 'SB' and resid 29 through 37 removed outlier: 3.948A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.234A pdb=" N LEUSB 83 " --> pdb=" O TYRSB 79 " (cutoff:3.500A) Proline residue: SB 84 - end of helix Processing helix chain 'SB' and resid 94 through 114 Processing helix chain 'SB' and resid 115 through 120 removed outlier: 3.552A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.766A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.519A pdb=" N HISSB 198 " --> pdb=" O VALSB 194 " (cutoff:3.500A) Processing helix chain 'SB' and resid 202 through 215 removed outlier: 3.633A pdb=" N GLUSB 213 " --> pdb=" O ARGSB 209 " (cutoff:3.500A) Processing helix chain 'SB' and resid 216 through 224 Processing helix chain 'SB' and resid 225 through 230 removed outlier: 4.495A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SERSB 230 " --> pdb=" O TYRSB 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 225 through 230' Processing helix chain 'SB' and resid 232 through 251 removed outlier: 3.506A pdb=" N METSB 236 " --> pdb=" O THRSB 232 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLUSB 238 " --> pdb=" O ASPSB 234 " (cutoff:3.500A) Proline residue: SB 251 - end of helix Processing helix chain 'SB' and resid 272 through 297 removed outlier: 3.587A pdb=" N VALSB 280 " --> pdb=" O LYSSB 276 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.968A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.881A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.296A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 3.509A pdb=" N LEUSC 286 " --> pdb=" O TYRSC 282 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 282 through 287' Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.613A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALASD 72 " --> pdb=" O GLUSD 68 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.651A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.254A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.959A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.218A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.658A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.511A pdb=" N TYRSE 71 " --> pdb=" O ARGSE 67 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 5.030A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.822A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 122 removed outlier: 5.502A pdb=" N ALASE 122 " --> pdb=" O ALASE 118 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 169 through 178 Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.917A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 4.836A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.826A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.125A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.528A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLYSF 13 " --> pdb=" O ARGSF 9 " (cutoff:3.500A) Processing helix chain 'SF' and resid 33 through 39 Processing helix chain 'SF' and resid 103 through 108 removed outlier: 3.691A pdb=" N METSF 107 " --> pdb=" O PROSF 103 " (cutoff:3.500A) Proline residue: SF 108 - end of helix No H-bonds generated for 'chain 'SF' and resid 103 through 108' Processing helix chain 'SF' and resid 181 through 193 removed outlier: 3.555A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.876A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASNSF 205 " --> pdb=" O GLYSF 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 200 through 205' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 4.076A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.516A pdb=" N THRSG 165 " --> pdb=" O ILESG 161 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.282A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.835A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.863A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 Processing helix chain 'SH' and resid 154 through 180 removed outlier: 3.548A pdb=" N GLYSH 180 " --> pdb=" O LEUSH 176 " (cutoff:3.500A) Processing helix chain 'SI' and resid 23 through 53 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 4.128A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 removed outlier: 3.547A pdb=" N ALASI 117 " --> pdb=" O GLNSI 113 " (cutoff:3.500A) Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 4.140A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.758A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.270A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARGSI 230 " --> pdb=" O ALASI 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 225 through 230' Processing helix chain 'SI' and resid 231 through 237 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.734A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.183A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.652A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.814A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.684A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.491A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SL' and resid 32 through 51 removed outlier: 5.962A pdb=" N LYSSL 51 " --> pdb=" O CYSSL 47 " (cutoff:3.500A) Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.863A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 166 removed outlier: 5.097A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 4.231A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 241 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.660A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 12 through 17 Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 removed outlier: 3.701A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 4.199A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Proline residue: SM 77 - end of helix Processing helix chain 'SM' and resid 78 through 99 Processing helix chain 'SM' and resid 100 through 111 removed outlier: 3.519A pdb=" N ARGSM 106 " --> pdb=" O ASNSM 102 " (cutoff:3.500A) Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 148 removed outlier: 3.594A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHESM 147 " --> pdb=" O LEUSM 143 " (cutoff:3.500A) Proline residue: SM 148 - end of helix Processing helix chain 'SM' and resid 154 through 176 Processing helix chain 'SM' and resid 217 through 243 removed outlier: 3.786A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 267 through 279 removed outlier: 4.417A pdb=" N CYSSM 272 " --> pdb=" O ASPSM 268 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N METSM 273 " --> pdb=" O SERSM 269 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.791A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.879A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.353A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.480A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 20 through 37 Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 3.500A pdb=" N ILESQ 56 " --> pdb=" O LYSSQ 52 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALASQ 59 " --> pdb=" O ASPSQ 55 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 removed outlier: 3.676A pdb=" N METSQ 73 " --> pdb=" O LYSSQ 69 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 4.173A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.120A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.320A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 4.986A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 418' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 3.932A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 3.912A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.678A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.826A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLNSR 486 " --> pdb=" O GLNSR 482 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 3.908A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYSSR 514 " --> pdb=" O ARGSR 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 509 through 514' Processing helix chain 'SR' and resid 516 through 528 removed outlier: 3.665A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.700A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.208A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.923A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N METSR 600 " --> pdb=" O ALASR 596 " (cutoff:3.500A) Processing helix chain 'SR' and resid 618 through 623 Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.703A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.528A pdb=" N ALASV 58 " --> pdb=" O ALASV 54 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.573A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 130 removed outlier: 4.105A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYSSV 125 " --> pdb=" O VALSV 121 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BE' and resid 34 through 37 removed outlier: 6.069A pdb=" N PHEBE 34 " --> pdb=" O VALBE 89 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILEBE 135 " --> pdb=" O ARGBE 90 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N METBE 136 " --> pdb=" O METBE 52 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYSBE 49 " --> pdb=" O SERBE 168 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARGBE 162 " --> pdb=" O ASPBE 55 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BE' and resid 189 through 192 removed outlier: 5.399A pdb=" N ARGBE 189 " --> pdb=" O ILEBE 200 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'L5' and resid 48 through 51 removed outlier: 5.273A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'L5' and resid 92 through 95 Processing sheet with id= 5, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 6, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 7, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.549A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.618A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.373A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.730A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 16 through 20 Processing sheet with id= 12, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.483A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LA' and resid 124 through 131 removed outlier: 4.070A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 15, first strand: chain 'LB' and resid 98 through 101 Processing sheet with id= 16, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.452A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.151A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.675A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LE' and resid 39 through 42 removed outlier: 3.903A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 21, first strand: chain 'LF' and resid 61 through 65 removed outlier: 5.952A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LG' and resid 76 through 80 removed outlier: 6.769A pdb=" N METLG 62 " --> pdb=" O ILELG 40 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARGLG 83 " --> pdb=" O ALALG 102 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.832A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LH' and resid 95 through 100 removed outlier: 4.052A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.647A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.536A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALLI 79 " --> pdb=" O TYRLI 74 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.637A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.159A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.095A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.347A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 45 through 50 removed outlier: 5.256A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LN' and resid 53 through 59 Processing sheet with id= 33, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.735A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 179 through 184 removed outlier: 4.541A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.518A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.366A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.353A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.913A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 40, first strand: chain 'LR' and resid 19 through 24 removed outlier: 5.210A pdb=" N LYSLR 19 " --> pdb=" O THRLR 35 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LT' and resid 46 through 49 removed outlier: 5.044A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARGLT 76 " --> pdb=" O ARGLT 85 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.720A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.535A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LY' and resid 2 through 5 removed outlier: 3.668A pdb=" N ARGLY 3 " --> pdb=" O LEULY 42 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.885A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.566A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.559A pdb=" N TYRSB 145 " --> pdb=" O TYRSB 49 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.398A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 50, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.419A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SD' and resid 158 through 161 removed outlier: 6.742A pdb=" N GLYSD 158 " --> pdb=" O LEUSD 169 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SE' and resid 180 through 185 removed outlier: 3.529A pdb=" N LEUSE 154 " --> pdb=" O PHESE 204 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.518A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SF' and resid 110 through 114 removed outlier: 3.962A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYSSF 145 " --> pdb=" O ASNSF 140 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.421A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.376A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 59, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.682A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.634A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLYSG 87 " --> pdb=" O VALSG 187 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'SH' and resid 72 through 77 removed outlier: 3.806A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.533A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 64, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 65, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 66, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 67, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.275A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SL' and resid 127 through 130 removed outlier: 3.644A pdb=" N GLNSL 128 " --> pdb=" O ILESL 95 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SL' and resid 210 through 217 removed outlier: 6.182A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.587A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 72, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 3.652A pdb=" N THRSQ 105 " --> pdb=" O TYRSQ 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYRSQ 39 " --> pdb=" O THRSQ 105 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THRSQ 203 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.578A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.056A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.367A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SV' and resid 18 through 22 2736 hydrogen bonds defined for protein. 8132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3075 hydrogen bonds 5256 hydrogen bond angles 0 basepair planarities 1160 basepair parallelities 1839 stacking parallelities Total time for adding SS restraints: 357.41 Time building geometry restraints manager: 62.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 15190 1.30 - 1.43: 64970 1.43 - 1.56: 71110 1.56 - 1.68: 7417 1.68 - 1.81: 453 Bond restraints: 159140 Sorted by residual: bond pdb=" C2' A2ML32401 " pdb=" C1' A2ML32401 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML31871 " pdb=" C1' A2ML31871 " ideal model delta sigma weight residual 1.305 1.549 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C2' A2ML3 398 " pdb=" C1' A2ML3 398 " ideal model delta sigma weight residual 1.305 1.546 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C2' A2ML33825 " pdb=" C1' A2ML33825 " ideal model delta sigma weight residual 1.305 1.545 -0.240 2.00e-02 2.50e+03 1.44e+02 ... (remaining 159135 not shown) Histogram of bond angle deviations from ideal: 85.21 - 95.31: 12 95.31 - 105.42: 18538 105.42 - 115.52: 109285 115.52 - 125.63: 91589 125.63 - 135.73: 13193 Bond angle restraints: 232617 Sorted by residual: angle pdb=" C1' A2ML33867 " pdb=" N9 A2ML33867 " pdb=" C8 A2ML33867 " ideal model delta sigma weight residual 88.50 127.83 -39.33 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 127.37 -38.87 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 127.02 -38.52 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' A2ML33724 " pdb=" N9 A2ML33724 " pdb=" C8 A2ML33724 " ideal model delta sigma weight residual 88.50 126.92 -38.42 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C1' A2ML3 400 " pdb=" N9 A2ML3 400 " pdb=" C8 A2ML3 400 " ideal model delta sigma weight residual 88.50 126.89 -38.39 3.00e+00 1.11e-01 1.64e+02 ... (remaining 232612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 92735 35.81 - 71.63: 8493 71.63 - 107.44: 1310 107.44 - 143.26: 17 143.26 - 179.07: 13 Dihedral angle restraints: 102568 sinusoidal: 77881 harmonic: 24687 Sorted by residual: dihedral pdb=" C5' GL34305 " pdb=" C4' GL34305 " pdb=" C3' GL34305 " pdb=" O3' GL34305 " ideal model delta sinusoidal sigma weight residual 147.00 73.68 73.32 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C4' CL3 502 " pdb=" C3' CL3 502 " pdb=" C2' CL3 502 " pdb=" C1' CL3 502 " ideal model delta sinusoidal sigma weight residual -35.00 34.68 -69.68 1 8.00e+00 1.56e-02 9.79e+01 dihedral pdb=" C4' GL34305 " pdb=" C3' GL34305 " pdb=" C2' GL34305 " pdb=" C1' GL34305 " ideal model delta sinusoidal sigma weight residual -35.00 34.24 -69.24 1 8.00e+00 1.56e-02 9.68e+01 ... (remaining 102565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 26940 0.083 - 0.166: 1429 0.166 - 0.249: 76 0.249 - 0.331: 7 0.331 - 0.414: 17 Chirality restraints: 28469 Sorted by residual: chirality pdb=" C2' A2ML34571 " pdb=" C3' A2ML34571 " pdb=" O2' A2ML34571 " pdb=" C1' A2ML34571 " both_signs ideal model delta sigma weight residual False -2.39 -2.81 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C2' A2ML32787 " pdb=" C3' A2ML32787 " pdb=" O2' A2ML32787 " pdb=" C1' A2ML32787 " both_signs ideal model delta sigma weight residual False -2.39 -2.81 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' GL34305 " pdb=" C4' GL34305 " pdb=" O3' GL34305 " pdb=" C2' GL34305 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 28466 not shown) Planarity restraints: 15655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.925 2.00e-02 2.50e+03 6.23e-01 8.73e+03 pdb=" C4' OMGL34228 " -0.209 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.711 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.175 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.998 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.627 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.683 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.446 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL33887 " 0.017 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' OMCL33887 " 0.484 2.00e-02 2.50e+03 pdb=" O4' OMCL33887 " 0.853 2.00e-02 2.50e+03 pdb=" C3' OMCL33887 " -0.574 2.00e-02 2.50e+03 pdb=" O3' OMCL33887 " -0.552 2.00e-02 2.50e+03 pdb=" C2' OMCL33887 " -0.268 2.00e-02 2.50e+03 pdb=" O2' OMCL33887 " 0.835 2.00e-02 2.50e+03 pdb=" C1' OMCL33887 " 0.175 2.00e-02 2.50e+03 pdb=" N1 OMCL33887 " -0.970 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.053 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' OMGL34494 " -0.456 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.709 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.632 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.200 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.947 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.205 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.944 2.00e-02 2.50e+03 ... (remaining 15652 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 1568 2.58 - 3.36: 168196 3.36 - 4.13: 456070 4.13 - 4.90: 688519 Nonbonded interactions: 1314354 Sorted by model distance: nonbonded pdb="MG MGL36063 " pdb="MG MGL36070 " model vdw 1.041 1.300 nonbonded pdb=" OE1 GLNLW 30 " pdb="MG MGLW 102 " model vdw 1.902 2.170 nonbonded pdb=" OP1 CL33636 " pdb="MG MGL36045 " model vdw 1.947 2.170 nonbonded pdb=" OP2 A2ML32363 " pdb="MG MGL36036 " model vdw 1.951 2.170 nonbonded pdb=" OP2 AL31337 " pdb="MG MGL36009 " model vdw 1.952 2.170 ... (remaining 1314349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 26.750 Check model and map are aligned: 1.590 Set scattering table: 1.030 Process input model: 680.930 Find NCS groups from input model: 4.150 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.090 Load rotamer database and sin/cos tables:17.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 739.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 159140 Z= 0.544 Angle : 0.833 39.334 232617 Z= 0.373 Chirality : 0.043 0.414 28469 Planarity : 0.026 0.623 15655 Dihedral : 21.822 179.070 86600 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 8373 helix: 0.28 (0.09), residues: 3118 sheet: 0.12 (0.15), residues: 1088 loop : -0.21 (0.09), residues: 4167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRPSV 86 HIS 0.017 0.002 HISSE 159 PHE 0.029 0.002 PHELN 374 TYR 0.057 0.002 TYRLC 84 ARG 0.018 0.001 ARGLK 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1595 time to evaluate : 7.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 29 SER cc_start: 0.8849 (t) cc_final: 0.8259 (p) REVERT: L5 129 ASP cc_start: 0.7509 (p0) cc_final: 0.7257 (p0) REVERT: L6 8 MET cc_start: 0.8435 (mtt) cc_final: 0.8140 (mtt) REVERT: L7 158 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6734 (mt-10) REVERT: L8 59 ASP cc_start: 0.8150 (m-30) cc_final: 0.7949 (m-30) REVERT: LA 47 TYR cc_start: 0.8710 (t80) cc_final: 0.8481 (t80) REVERT: LI 53 ASP cc_start: 0.7942 (m-30) cc_final: 0.7733 (m-30) REVERT: LK 135 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8056 (mt-10) REVERT: LR 86 CYS cc_start: 0.6464 (m) cc_final: 0.6161 (m) REVERT: LU 32 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7264 (tpt170) REVERT: NL 141 ASN cc_start: 0.8737 (m110) cc_final: 0.8442 (m110) REVERT: NP 99 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8600 (tp-100) REVERT: SA 268 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7185 (mtp85) REVERT: SD 248 ASN cc_start: 0.8201 (t0) cc_final: 0.7962 (t0) REVERT: SG 113 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7118 (mt-10) REVERT: SG 143 GLU cc_start: 0.7436 (tt0) cc_final: 0.7235 (tt0) REVERT: SL 158 ASP cc_start: 0.7951 (t0) cc_final: 0.7740 (t0) REVERT: SR 482 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7389 (mm-40) REVERT: SV 66 ASP cc_start: 0.7586 (t70) cc_final: 0.7381 (t0) outliers start: 0 outliers final: 2 residues processed: 1595 average time/residue: 2.5493 time to fit residues: 5722.5989 Evaluate side-chains 1094 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1092 time to evaluate : 7.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain NL residue 161 LEU Chi-restraints excluded: chain SK residue 74 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 1012 optimal weight: 5.9990 chunk 908 optimal weight: 2.9990 chunk 504 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 613 optimal weight: 0.0970 chunk 485 optimal weight: 3.9990 chunk 939 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 571 optimal weight: 0.0980 chunk 699 optimal weight: 0.9980 chunk 1088 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 92 HIS ** BE 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 177 ASN L5 112 HIS L6 67 HIS L6 175 ASN L7 199 HIS L9 8 GLN LA 10 ASN LB 188 ASN LC 122 HIS LE 127 GLN LE 131 GLN LE 144 ASN LG 27 ASN LG 36 ASN LH 107 HIS LI 86 GLN LK 25 HIS LK 85 GLN LL 83 ASN LM 7 HIS LM 12 GLN LM 49 HIS LN 42 HIS LN 121 ASN LN 322 HIS LO 33 GLN LO 73 HIS LS 65 GLN LT 55 ASN NK 21 ASN NL 124 ASN NP 13 HIS NP 18 GLN SB 138 GLN SC 101 ASN SC 136 HIS SC 190 HIS SC 211 HIS SD 63 GLN SE 85 GLN SE 100 HIS SE 141 ASN SE 149 ASN SF 139 HIS SF 140 ASN SG 39 ASN SG 40 HIS SG 188 GLN SI 136 ASN SK 83 HIS SM 170 HIS SM 211 HIS SM 245 HIS SM 320 GLN SR 361 HIS SR 504 GLN ** SR 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN SR 612 HIS SV 17 HIS SV 39 ASN SV 110 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 159140 Z= 0.146 Angle : 0.693 19.550 232617 Z= 0.376 Chirality : 0.034 0.298 28469 Planarity : 0.007 0.131 15655 Dihedral : 23.109 179.114 68543 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.87 % Allowed : 10.02 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8373 helix: 1.62 (0.09), residues: 3186 sheet: 0.43 (0.15), residues: 1086 loop : 0.02 (0.09), residues: 4101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPNK 96 HIS 0.005 0.001 HISL7 199 PHE 0.030 0.001 PHESH 165 TYR 0.025 0.001 TYRBE 75 ARG 0.009 0.000 ARGSE 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1184 time to evaluate : 8.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 29 SER cc_start: 0.8642 (t) cc_final: 0.8424 (p) REVERT: L5 129 ASP cc_start: 0.7464 (p0) cc_final: 0.7198 (p0) REVERT: L6 8 MET cc_start: 0.8414 (mtt) cc_final: 0.8191 (mtt) REVERT: L8 108 ASP cc_start: 0.7478 (m-30) cc_final: 0.7275 (m-30) REVERT: LD 136 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7687 (mtm110) REVERT: LF 44 GLN cc_start: 0.8394 (mt0) cc_final: 0.7052 (mt0) REVERT: LI 25 ILE cc_start: 0.8381 (mp) cc_final: 0.8169 (mm) REVERT: LK 135 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7922 (mt-10) REVERT: LO 31 TYR cc_start: 0.8523 (t80) cc_final: 0.8205 (t80) REVERT: LP 46 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8156 (mt) REVERT: LX 26 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8652 (t) REVERT: LY 16 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7905 (mtp85) REVERT: NL 343 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8242 (ttp80) REVERT: NL 404 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6785 (mtp-110) REVERT: SA 268 ARG cc_start: 0.7483 (mtp-110) cc_final: 0.7163 (mtp85) REVERT: SC 270 TYR cc_start: 0.8693 (t80) cc_final: 0.8416 (t80) REVERT: SD 220 MET cc_start: 0.7112 (ttt) cc_final: 0.6814 (ttt) REVERT: SD 248 ASN cc_start: 0.8108 (t0) cc_final: 0.7880 (t0) REVERT: SE 45 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8670 (mp) REVERT: SE 252 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8238 (mtpp) REVERT: SI 39 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: SM 193 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: SM 265 TYR cc_start: 0.8400 (m-80) cc_final: 0.7969 (m-80) REVERT: SR 523 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6612 (tm-30) outliers start: 136 outliers final: 50 residues processed: 1250 average time/residue: 2.1890 time to fit residues: 3972.8188 Evaluate side-chains 1103 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1045 time to evaluate : 7.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 57 VAL Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LF residue 55 ASN Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LH residue 111 GLN Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LN residue 397 ILE Chi-restraints excluded: chain LO residue 13 SER Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 99 GLN Chi-restraints excluded: chain NL residue 343 ARG Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain SA residue 84 THR Chi-restraints excluded: chain SB residue 34 LYS Chi-restraints excluded: chain SC residue 112 MET Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 84 THR Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SL residue 77 GLU Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SM residue 193 GLU Chi-restraints excluded: chain SR residue 446 ILE Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 547 ARG Chi-restraints excluded: chain SR residue 600 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 605 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 chunk 906 optimal weight: 5.9990 chunk 741 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 1090 optimal weight: 3.9990 chunk 1178 optimal weight: 7.9990 chunk 971 optimal weight: 8.9990 chunk 1081 optimal weight: 2.9990 chunk 371 optimal weight: 10.0000 chunk 875 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 147 HIS BE 177 ASN L5 168 GLN L6 67 HIS L7 184 ASN L8 69 HIS L9 109 HIS LA 25 HIS LA 75 GLN LA 116 HIS LB 188 ASN LC 37 HIS LC 50 GLN LE 127 GLN LE 131 GLN ** LF 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 55 ASN LG 36 ASN LI 65 GLN LK 25 HIS LK 60 HIS LK 85 GLN LN 121 ASN LQ 117 GLN LT 55 ASN LX 56 HIS NK 21 ASN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN SB 81 HIS SB 229 ASN SB 244 HIS SD 63 GLN SE 100 HIS SG 106 GLN SG 162 GLN SI 225 HIS SK 145 GLN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 211 HIS ** SM 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SR 414 GLN SR 504 GLN SR 538 HIS SR 542 GLN SV 87 ASN SV 132 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 159140 Z= 0.492 Angle : 0.816 20.698 232617 Z= 0.425 Chirality : 0.044 0.342 28469 Planarity : 0.008 0.145 15655 Dihedral : 23.140 179.846 68539 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.16 % Allowed : 11.91 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8373 helix: 1.40 (0.09), residues: 3202 sheet: 0.35 (0.15), residues: 1065 loop : -0.26 (0.09), residues: 4106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRPNK 96 HIS 0.012 0.002 HISLK 39 PHE 0.031 0.003 PHESH 165 TYR 0.036 0.003 TYRSE 102 ARG 0.015 0.001 ARGLV 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1057 time to evaluate : 8.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 29 SER cc_start: 0.8890 (t) cc_final: 0.8559 (p) REVERT: L5 35 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7051 (ttm110) REVERT: L5 129 ASP cc_start: 0.7406 (p0) cc_final: 0.7186 (p0) REVERT: L6 8 MET cc_start: 0.8432 (mtt) cc_final: 0.8072 (mtt) REVERT: L6 107 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8496 (m) REVERT: L6 111 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: L6 184 MET cc_start: 0.8127 (mtp) cc_final: 0.7549 (mtp) REVERT: L8 126 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7841 (mm-30) REVERT: LA 107 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8184 (mt) REVERT: LD 30 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8315 (m-40) REVERT: LI 40 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: LK 21 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7902 (mmt90) REVERT: LK 135 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8049 (mt-10) REVERT: LL 28 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: LL 67 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7506 (ptm-80) REVERT: LM 114 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8167 (tptp) REVERT: LO 42 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8592 (mtmt) REVERT: LQ 81 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8658 (p0) REVERT: LR 86 CYS cc_start: 0.6587 (m) cc_final: 0.6223 (m) REVERT: LT 104 MET cc_start: 0.8562 (mmt) cc_final: 0.8205 (mmt) REVERT: LV 78 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7633 (mmm160) REVERT: LY 16 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7981 (mtp85) REVERT: NL 343 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8437 (ttp80) REVERT: NL 404 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6853 (mtp-110) REVERT: SA 268 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.7058 (mtp85) REVERT: SD 248 ASN cc_start: 0.8258 (t0) cc_final: 0.8025 (t0) REVERT: SE 45 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8840 (mp) REVERT: SE 252 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8366 (mtpp) REVERT: SL 94 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7429 (p0) REVERT: SR 523 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: SV 93 MET cc_start: 0.7177 (ptt) cc_final: 0.6954 (ptm) outliers start: 230 outliers final: 131 residues processed: 1170 average time/residue: 2.1959 time to fit residues: 3732.6586 Evaluate side-chains 1161 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1014 time to evaluate : 7.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 62 SER Chi-restraints excluded: chain BE residue 193 ASP Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 35 ARG Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 57 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 111 GLN Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 44 GLN Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 100 SER Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 69 LYS Chi-restraints excluded: chain LF residue 79 SER Chi-restraints excluded: chain LF residue 106 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LJ residue 94 THR Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 21 ARG Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 67 ARG Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 53 MET Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 13 SER Chi-restraints excluded: chain LO residue 42 LYS Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 107 SER Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 20 ASN Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LW residue 24 SER Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 44 THR Chi-restraints excluded: chain LY residue 46 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 99 GLN Chi-restraints excluded: chain NL residue 343 ARG Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 37 VAL Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 184 ILE Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 84 THR Chi-restraints excluded: chain SF residue 111 THR Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 156 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SL residue 77 GLU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 547 ARG Chi-restraints excluded: chain SR residue 591 THR Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 1077 optimal weight: 6.9990 chunk 820 optimal weight: 0.9990 chunk 566 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 520 optimal weight: 1.9990 chunk 732 optimal weight: 5.9990 chunk 1094 optimal weight: 3.9990 chunk 1158 optimal weight: 0.9990 chunk 571 optimal weight: 0.9990 chunk 1037 optimal weight: 0.6980 chunk 312 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BE 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 177 ASN L5 168 GLN ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 67 HIS LA 10 ASN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 188 ASN LE 131 GLN LI 65 GLN ** LJ 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 25 HIS LK 60 HIS LN 175 GLN LP 30 HIS LP 121 ASN LT 55 ASN LU 92 ASN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 244 HIS ** SE 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN ** SL 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 211 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 159140 Z= 0.140 Angle : 0.662 19.530 232617 Z= 0.364 Chirality : 0.033 0.300 28469 Planarity : 0.007 0.127 15655 Dihedral : 22.993 179.073 68539 Min Nonbonded Distance : 1.098 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.08 % Allowed : 13.56 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8373 helix: 1.92 (0.09), residues: 3187 sheet: 0.44 (0.15), residues: 1096 loop : -0.07 (0.09), residues: 4090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLW 49 HIS 0.004 0.001 HISLK 25 PHE 0.019 0.001 PHELF 39 TYR 0.031 0.001 TYRBE 75 ARG 0.010 0.000 ARGSH 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1103 time to evaluate : 8.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8819 (mp) REVERT: L5 31 ASP cc_start: 0.6141 (t0) cc_final: 0.5739 (t0) REVERT: L5 129 ASP cc_start: 0.7418 (p0) cc_final: 0.7184 (p0) REVERT: L6 8 MET cc_start: 0.8433 (mtt) cc_final: 0.8142 (mtt) REVERT: LD 112 SER cc_start: 0.8036 (m) cc_final: 0.7804 (p) REVERT: LJ 88 ASP cc_start: 0.7680 (p0) cc_final: 0.7459 (p0) REVERT: LO 31 TYR cc_start: 0.8589 (t80) cc_final: 0.8320 (t80) REVERT: LQ 5 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7743 (mmm-85) REVERT: LT 104 MET cc_start: 0.8468 (mmt) cc_final: 0.8168 (mmp) REVERT: LZ 11 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7988 (ttp-170) REVERT: NK 97 MET cc_start: 0.7052 (ttm) cc_final: 0.6824 (ttp) REVERT: NL 404 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6772 (mtp-110) REVERT: SC 270 TYR cc_start: 0.8681 (t80) cc_final: 0.8416 (t80) REVERT: SD 32 ARG cc_start: 0.7490 (ptp-170) cc_final: 0.7276 (ptt180) REVERT: SD 248 ASN cc_start: 0.8097 (t0) cc_final: 0.7868 (t0) REVERT: SK 1 MET cc_start: 0.5468 (ttt) cc_final: 0.5256 (ttp) REVERT: SR 523 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: SV 117 GLU cc_start: 0.6712 (tp30) cc_final: 0.6468 (tp30) outliers start: 151 outliers final: 72 residues processed: 1184 average time/residue: 2.1245 time to fit residues: 3660.0245 Evaluate side-chains 1099 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1023 time to evaluate : 7.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LK residue 63 LEU Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LQ residue 42 ASP Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LW residue 24 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 99 GLN Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 14 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 965 optimal weight: 2.9990 chunk 657 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 862 optimal weight: 5.9990 chunk 478 optimal weight: 1.9990 chunk 988 optimal weight: 2.9990 chunk 801 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 591 optimal weight: 5.9990 chunk 1040 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 177 ASN L5 168 GLN L6 67 HIS L7 199 HIS LA 75 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 188 ASN LE 127 GLN LE 131 GLN LI 65 GLN LK 25 HIS LP 121 ASN LT 55 ASN LU 92 ASN LZ 25 GLN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 244 HIS SD 24 ASN SE 85 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SL 218 HIS SM 211 HIS SR 414 GLN ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 159140 Z= 0.288 Angle : 0.703 19.884 232617 Z= 0.378 Chirality : 0.036 0.315 28469 Planarity : 0.007 0.136 15655 Dihedral : 22.980 179.122 68539 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.68 % Allowed : 14.22 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 8373 helix: 1.85 (0.09), residues: 3199 sheet: 0.42 (0.16), residues: 1084 loop : -0.16 (0.09), residues: 4090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPLW 49 HIS 0.007 0.001 HISLE 58 PHE 0.019 0.002 PHEL7 47 TYR 0.027 0.002 TYRSE 102 ARG 0.012 0.001 ARGLS 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1047 time to evaluate : 8.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8819 (mp) REVERT: L5 129 ASP cc_start: 0.7402 (p0) cc_final: 0.7190 (p0) REVERT: L6 8 MET cc_start: 0.8430 (mtt) cc_final: 0.8110 (mtt) REVERT: L6 69 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7958 (mptp) REVERT: L6 184 MET cc_start: 0.8012 (mtp) cc_final: 0.7210 (mtp) REVERT: L7 179 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8229 (mtpm) REVERT: L8 108 ASP cc_start: 0.7573 (m-30) cc_final: 0.7307 (m-30) REVERT: L9 24 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7258 (ttt180) REVERT: LD 112 SER cc_start: 0.8086 (m) cc_final: 0.7852 (p) REVERT: LF 30 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: LG 48 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7844 (ttt90) REVERT: LI 40 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: LL 28 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: LN 59 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: LO 31 TYR cc_start: 0.8652 (t80) cc_final: 0.8339 (t80) REVERT: LQ 5 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7741 (mmm-85) REVERT: LT 104 MET cc_start: 0.8530 (mmt) cc_final: 0.8188 (mmt) REVERT: LX 47 MET cc_start: 0.8696 (mmt) cc_final: 0.8344 (mmt) REVERT: NK 97 MET cc_start: 0.7064 (ttm) cc_final: 0.6813 (ttp) REVERT: NL 364 ARG cc_start: 0.7929 (mpp-170) cc_final: 0.7649 (mtt-85) REVERT: NL 404 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6788 (mtp-110) REVERT: SC 270 TYR cc_start: 0.8748 (t80) cc_final: 0.8486 (t80) REVERT: SD 248 ASN cc_start: 0.8142 (t0) cc_final: 0.7902 (t0) REVERT: SE 45 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8766 (mp) REVERT: SE 211 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: SK 1 MET cc_start: 0.5476 (ttt) cc_final: 0.5216 (ttp) REVERT: SK 67 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7501 (ptp90) REVERT: SL 221 MET cc_start: 0.7046 (mtp) cc_final: 0.6802 (mtm) REVERT: SR 523 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: SR 575 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8168 (ptp-170) REVERT: SV 117 GLU cc_start: 0.6701 (tp30) cc_final: 0.6457 (tp30) outliers start: 195 outliers final: 115 residues processed: 1160 average time/residue: 2.1753 time to fit residues: 3669.6284 Evaluate side-chains 1152 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1021 time to evaluate : 7.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L8 residue 44 GLN Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 84 THR Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L9 residue 24 ARG Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 100 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 30 GLU Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 106 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 48 ARG Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 1 MET Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 8 THR Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 185 VAL Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 338 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 42 LYS Chi-restraints excluded: chain LO residue 68 LYS Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LW residue 24 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 287 THR Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 37 VAL Chi-restraints excluded: chain SB residue 268 ARG Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 184 ILE Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 14 SER Chi-restraints excluded: chain SF residue 111 THR Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 16 VAL Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 591 THR Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 389 optimal weight: 10.0000 chunk 1043 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 680 optimal weight: 8.9990 chunk 286 optimal weight: 8.9990 chunk 1160 optimal weight: 40.0000 chunk 963 optimal weight: 0.0770 chunk 537 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 383 optimal weight: 4.9990 chunk 609 optimal weight: 5.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 177 ASN L5 168 GLN L6 67 HIS L7 42 ASN L7 184 ASN L7 199 HIS LA 75 GLN LB 125 GLN LB 188 ASN LE 127 GLN LE 131 GLN ** LF 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 14 ASN LK 25 HIS LK 60 HIS LP 121 ASN LQ 101 HIS LT 55 ASN LU 92 ASN LZ 25 GLN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 244 HIS SD 63 GLN SE 85 GLN SG 106 GLN SK 93 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 211 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 159140 Z= 0.476 Angle : 0.801 20.560 232617 Z= 0.419 Chirality : 0.043 0.345 28469 Planarity : 0.008 0.144 15655 Dihedral : 23.092 179.987 68539 Min Nonbonded Distance : 0.994 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.55 % Allowed : 14.35 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8373 helix: 1.51 (0.09), residues: 3193 sheet: 0.35 (0.16), residues: 1056 loop : -0.35 (0.09), residues: 4124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLW 49 HIS 0.011 0.002 HISLK 39 PHE 0.025 0.002 PHEL5 130 TYR 0.032 0.002 TYRSE 102 ARG 0.013 0.001 ARGLV 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1024 time to evaluate : 8.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8948 (mp) REVERT: L6 8 MET cc_start: 0.8381 (mtt) cc_final: 0.7996 (mtt) REVERT: L6 69 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7998 (mptp) REVERT: L6 184 MET cc_start: 0.8100 (mtp) cc_final: 0.7369 (mtp) REVERT: L7 93 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8111 (mtmt) REVERT: L8 108 ASP cc_start: 0.7411 (m-30) cc_final: 0.7206 (m-30) REVERT: L8 126 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7931 (tm-30) REVERT: L9 24 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7299 (ttt-90) REVERT: LA 115 GLU cc_start: 0.7577 (tt0) cc_final: 0.7151 (tt0) REVERT: LB 93 GLN cc_start: 0.7458 (mp10) cc_final: 0.7147 (mp10) REVERT: LB 147 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: LD 112 SER cc_start: 0.8193 (m) cc_final: 0.7932 (p) REVERT: LF 30 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: LI 40 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: LI 113 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7145 (pttm) REVERT: LK 21 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7941 (mmt90) REVERT: LL 28 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: LQ 5 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7780 (mmm-85) REVERT: LR 86 CYS cc_start: 0.6540 (m) cc_final: 0.6160 (m) REVERT: LT 104 MET cc_start: 0.8583 (mmt) cc_final: 0.8213 (mmt) REVERT: LX 26 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8625 (t) REVERT: LX 47 MET cc_start: 0.8670 (mmt) cc_final: 0.8278 (mmt) REVERT: NL 404 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.6826 (mtp-110) REVERT: SB 265 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7379 (ttt90) REVERT: SC 270 TYR cc_start: 0.8818 (t80) cc_final: 0.8553 (t80) REVERT: SD 248 ASN cc_start: 0.8244 (t0) cc_final: 0.8004 (t0) REVERT: SE 45 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8821 (mp) REVERT: SE 211 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: SK 67 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7548 (ptp90) REVERT: SL 77 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: SL 221 MET cc_start: 0.7187 (mtp) cc_final: 0.6975 (mtm) REVERT: SM 220 MET cc_start: 0.8857 (mmm) cc_final: 0.8629 (mmt) REVERT: SR 447 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6669 (pmm) REVERT: SR 523 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: SR 575 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.6777 (ptp-170) REVERT: SV 117 GLU cc_start: 0.6740 (tp30) cc_final: 0.6511 (tp30) outliers start: 258 outliers final: 157 residues processed: 1166 average time/residue: 2.2083 time to fit residues: 3754.0523 Evaluate side-chains 1171 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 994 time to evaluate : 7.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 62 SER Chi-restraints excluded: chain BE residue 129 VAL Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L6 residue 181 SER Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L7 residue 153 THR Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 84 THR Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L9 residue 24 ARG Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 100 SER Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 30 GLU Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LF residue 63 ILE Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 106 SER Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 48 ARG Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 1 MET Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LI residue 113 LYS Chi-restraints excluded: chain LJ residue 94 THR Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 21 ARG Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LK residue 95 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 101 LYS Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 8 THR Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 53 MET Chi-restraints excluded: chain LN residue 185 VAL Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 338 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LO residue 68 LYS Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 107 SER Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 42 ASP Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 20 ASN Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LW residue 24 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 44 THR Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 358 LEU Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 287 THR Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 37 VAL Chi-restraints excluded: chain SB residue 93 THR Chi-restraints excluded: chain SB residue 265 ARG Chi-restraints excluded: chain SB residue 268 ARG Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SD residue 30 ILE Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 184 ILE Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 14 SER Chi-restraints excluded: chain SF residue 111 THR Chi-restraints excluded: chain SF residue 130 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 16 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 38 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 95 SER Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SL residue 77 GLU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SR residue 381 VAL Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 447 MET Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SR residue 591 THR Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 34 SER Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 1118 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 660 optimal weight: 0.9990 chunk 847 optimal weight: 3.9990 chunk 656 optimal weight: 0.9990 chunk 976 optimal weight: 2.9990 chunk 647 optimal weight: 0.9990 chunk 1155 optimal weight: 50.0000 chunk 723 optimal weight: 0.9990 chunk 704 optimal weight: 1.9990 chunk 533 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 177 ASN L5 168 GLN L6 67 HIS L7 184 ASN L7 199 HIS LA 75 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 188 ASN LE 127 GLN LE 131 GLN LI 14 ASN LI 65 GLN LK 25 HIS LK 60 HIS LL 83 ASN LP 121 ASN LT 55 ASN LU 92 ASN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NP 32 HIS SE 85 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SM 211 HIS SR 414 GLN ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 159140 Z= 0.147 Angle : 0.664 19.463 232617 Z= 0.364 Chirality : 0.033 0.301 28469 Planarity : 0.007 0.128 15655 Dihedral : 22.944 179.380 68539 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.34 % Allowed : 15.90 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8373 helix: 1.94 (0.09), residues: 3190 sheet: 0.46 (0.16), residues: 1079 loop : -0.18 (0.09), residues: 4104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLW 49 HIS 0.005 0.001 HISLK 25 PHE 0.026 0.001 PHESR 376 TYR 0.017 0.001 TYRSE 102 ARG 0.015 0.000 ARGLD 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1058 time to evaluate : 8.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8846 (mp) REVERT: L6 8 MET cc_start: 0.8436 (mtt) cc_final: 0.8135 (mtt) REVERT: L6 69 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7947 (mptp) REVERT: L6 184 MET cc_start: 0.7992 (mtp) cc_final: 0.7194 (mtp) REVERT: L8 108 ASP cc_start: 0.7492 (m-30) cc_final: 0.7277 (m-30) REVERT: L8 126 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7951 (tm-30) REVERT: L9 24 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7220 (ttt-90) REVERT: LA 115 GLU cc_start: 0.7539 (tt0) cc_final: 0.7114 (tt0) REVERT: LB 93 GLN cc_start: 0.7506 (mp10) cc_final: 0.7181 (mp10) REVERT: LC 161 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8030 (mtt180) REVERT: LD 112 SER cc_start: 0.8165 (m) cc_final: 0.7945 (p) REVERT: LD 136 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7254 (mtm110) REVERT: LE 107 LYS cc_start: 0.7767 (mmmm) cc_final: 0.7503 (mmmm) REVERT: LG 48 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7502 (ttt90) REVERT: LI 113 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6839 (pttm) REVERT: LK 21 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7780 (mmt90) REVERT: LL 28 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: LM 43 MET cc_start: 0.8259 (ttm) cc_final: 0.8040 (ttp) REVERT: LP 56 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: LQ 5 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7713 (mmm-85) REVERT: LQ 25 SER cc_start: 0.8978 (p) cc_final: 0.8726 (t) REVERT: LT 104 MET cc_start: 0.8502 (mmt) cc_final: 0.8147 (mmt) REVERT: LX 47 MET cc_start: 0.8647 (mmt) cc_final: 0.8238 (mmt) REVERT: NL 404 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6738 (mtp-110) REVERT: SB 265 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7503 (ttt90) REVERT: SC 268 GLN cc_start: 0.8251 (pt0) cc_final: 0.8043 (pt0) REVERT: SC 270 TYR cc_start: 0.8733 (t80) cc_final: 0.8449 (t80) REVERT: SD 248 ASN cc_start: 0.8079 (t0) cc_final: 0.7834 (t0) REVERT: SE 45 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8675 (mp) REVERT: SE 211 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: SG 86 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6898 (mt) REVERT: SI 39 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: SK 67 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7552 (ptp90) REVERT: SR 523 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: SV 117 GLU cc_start: 0.6652 (tp30) cc_final: 0.6395 (tp30) outliers start: 170 outliers final: 102 residues processed: 1153 average time/residue: 2.0885 time to fit residues: 3523.7338 Evaluate side-chains 1131 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1011 time to evaluate : 7.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 129 VAL Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L7 residue 153 THR Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 24 ARG Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 161 ARG Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 106 SER Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 48 ARG Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 113 LYS Chi-restraints excluded: chain LJ residue 94 THR Chi-restraints excluded: chain LK residue 21 ARG Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LO residue 68 LYS Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 56 GLU Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LQ residue 42 ASP Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LW residue 24 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain NL residue 286 GLN Chi-restraints excluded: chain NL residue 358 LEU Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 93 THR Chi-restraints excluded: chain SB residue 212 MET Chi-restraints excluded: chain SB residue 265 ARG Chi-restraints excluded: chain SB residue 268 ARG Chi-restraints excluded: chain SC residue 120 ASP Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 184 ILE Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 130 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 38 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SR residue 381 VAL Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 34 SER Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 714 optimal weight: 6.9990 chunk 461 optimal weight: 3.9990 chunk 690 optimal weight: 0.0570 chunk 348 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 734 optimal weight: 10.0000 chunk 787 optimal weight: 8.9990 chunk 571 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 908 optimal weight: 3.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 177 ASN L5 168 GLN L6 67 HIS L7 184 ASN ** L7 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 75 GLN LB 188 ASN LE 127 GLN LE 131 GLN LI 14 ASN LI 65 GLN LK 25 HIS LL 100 ASN LP 121 ASN LQ 102 ASN LT 55 ASN LU 92 ASN LZ 25 GLN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 244 HIS SE 85 GLN SG 106 GLN SG 162 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 211 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 159140 Z= 0.428 Angle : 0.770 20.134 232617 Z= 0.406 Chirality : 0.041 0.338 28469 Planarity : 0.008 0.141 15655 Dihedral : 23.003 179.690 68539 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.83 % Allowed : 15.92 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8373 helix: 1.67 (0.09), residues: 3189 sheet: 0.34 (0.16), residues: 1058 loop : -0.31 (0.09), residues: 4126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPLW 49 HIS 0.009 0.001 HISLE 58 PHE 0.027 0.002 PHESR 376 TYR 0.031 0.002 TYRSK 35 ARG 0.019 0.001 ARGLD 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1000 time to evaluate : 8.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8852 (mp) REVERT: L5 64 ARG cc_start: 0.8186 (ptm-80) cc_final: 0.7936 (ptm-80) REVERT: L6 8 MET cc_start: 0.8429 (mtt) cc_final: 0.8050 (mtt) REVERT: L6 69 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (mptp) REVERT: L6 184 MET cc_start: 0.8105 (mtp) cc_final: 0.7256 (mtp) REVERT: L8 126 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8011 (tm-30) REVERT: L9 24 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7312 (ttt-90) REVERT: LA 94 MET cc_start: 0.8223 (mtp) cc_final: 0.8022 (ttt) REVERT: LA 115 GLU cc_start: 0.7544 (tt0) cc_final: 0.7119 (tt0) REVERT: LD 112 SER cc_start: 0.8218 (m) cc_final: 0.7959 (p) REVERT: LI 40 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: LI 113 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.7054 (pttm) REVERT: LK 21 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7921 (mmt90) REVERT: LL 28 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: LP 56 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: LQ 5 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7774 (mmm-85) REVERT: LQ 81 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8617 (p0) REVERT: LR 86 CYS cc_start: 0.6577 (m) cc_final: 0.6209 (m) REVERT: LT 104 MET cc_start: 0.8552 (mmt) cc_final: 0.8138 (mmt) REVERT: NL 404 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.6826 (mtp-110) REVERT: SB 265 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7386 (ttt90) REVERT: SC 270 TYR cc_start: 0.8800 (t80) cc_final: 0.8516 (t80) REVERT: SD 248 ASN cc_start: 0.8177 (t0) cc_final: 0.7935 (t0) REVERT: SE 45 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8809 (mp) REVERT: SE 211 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: SG 86 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7214 (mp) REVERT: SK 67 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7558 (ptp90) REVERT: SK 157 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7719 (mm-40) REVERT: SL 77 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: SL 94 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7378 (p0) REVERT: SR 523 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: SR 575 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6865 (ptp-170) REVERT: SV 117 GLU cc_start: 0.6755 (tp30) cc_final: 0.6523 (tp30) outliers start: 206 outliers final: 131 residues processed: 1117 average time/residue: 2.1788 time to fit residues: 3537.9602 Evaluate side-chains 1136 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 984 time to evaluate : 7.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 129 VAL Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 136 LYS Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L7 residue 153 THR Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 24 ARG Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 100 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LF residue 106 SER Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 48 ARG Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 138 VAL Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 1 MET Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LI residue 113 LYS Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 21 ARG Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 8 THR Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 185 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 68 LYS Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 107 SER Chi-restraints excluded: chain LP residue 56 GLU Chi-restraints excluded: chain LP residue 64 ILE Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LW residue 24 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 44 THR Chi-restraints excluded: chain LY residue 46 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 286 GLN Chi-restraints excluded: chain NL residue 358 LEU Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain SA residue 287 THR Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 93 THR Chi-restraints excluded: chain SB residue 265 ARG Chi-restraints excluded: chain SB residue 268 ARG Chi-restraints excluded: chain SC residue 120 ASP Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 184 ILE Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 111 THR Chi-restraints excluded: chain SF residue 130 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 136 VAL Chi-restraints excluded: chain SG residue 16 VAL Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 156 THR Chi-restraints excluded: chain SI residue 38 THR Chi-restraints excluded: chain SI residue 39 GLN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 157 GLN Chi-restraints excluded: chain SL residue 77 GLU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SR residue 381 VAL Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 34 SER Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 1051 optimal weight: 1.9990 chunk 1107 optimal weight: 0.3980 chunk 1010 optimal weight: 0.9990 chunk 1076 optimal weight: 0.6980 chunk 1106 optimal weight: 10.0000 chunk 648 optimal weight: 4.9990 chunk 469 optimal weight: 0.9980 chunk 845 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 973 optimal weight: 0.9990 chunk 1018 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 177 ASN L5 168 GLN L6 67 HIS L7 96 GLN L7 184 ASN LA 75 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 77 ASN LB 188 ASN LE 127 GLN LE 131 GLN ** LF 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 14 ASN LI 65 GLN ** LK 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 21 ASN LL 83 ASN LP 121 ASN LT 55 ASN LU 92 ASN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 244 HIS SE 85 GLN SE 195 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SG 162 GLN SK 75 ASN SM 211 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 159140 Z= 0.132 Angle : 0.660 19.463 232617 Z= 0.362 Chirality : 0.032 0.292 28469 Planarity : 0.007 0.126 15655 Dihedral : 22.914 179.149 68539 Min Nonbonded Distance : 1.104 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.01 % Allowed : 16.91 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8373 helix: 2.01 (0.09), residues: 3194 sheet: 0.44 (0.16), residues: 1083 loop : -0.15 (0.09), residues: 4096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLW 49 HIS 0.006 0.001 HISLK 25 PHE 0.022 0.001 PHESR 376 TYR 0.020 0.001 TYRBE 75 ARG 0.014 0.000 ARGLN 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1042 time to evaluate : 8.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8833 (mp) REVERT: L5 64 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7810 (ptm-80) REVERT: L6 8 MET cc_start: 0.8428 (mtt) cc_final: 0.8118 (mtt) REVERT: LA 115 GLU cc_start: 0.7501 (tt0) cc_final: 0.7134 (tt0) REVERT: LD 112 SER cc_start: 0.8132 (m) cc_final: 0.7930 (p) REVERT: LI 40 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8016 (tm-30) REVERT: LI 113 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6816 (pttm) REVERT: LK 21 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7762 (mmt90) REVERT: LL 28 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: LM 43 MET cc_start: 0.8252 (ttm) cc_final: 0.8011 (ttp) REVERT: LQ 5 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7704 (mmm-85) REVERT: LT 104 MET cc_start: 0.8496 (mmt) cc_final: 0.8098 (mmt) REVERT: NL 404 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6732 (mtp-110) REVERT: SC 270 TYR cc_start: 0.8728 (t80) cc_final: 0.8439 (t80) REVERT: SD 248 ASN cc_start: 0.8039 (t0) cc_final: 0.7790 (t0) REVERT: SE 45 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8653 (mp) REVERT: SE 211 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: SG 86 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6915 (mt) REVERT: SH 156 THR cc_start: 0.7815 (p) cc_final: 0.7530 (t) REVERT: SK 67 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7533 (ptp90) REVERT: SL 94 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7230 (p0) REVERT: SR 523 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6908 (tm-30) outliers start: 146 outliers final: 96 residues processed: 1122 average time/residue: 2.1559 time to fit residues: 3537.6530 Evaluate side-chains 1112 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1004 time to evaluate : 7.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 129 VAL Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain BE residue 193 ASP Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 113 LYS Chi-restraints excluded: chain LJ residue 94 THR Chi-restraints excluded: chain LK residue 21 ARG Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 185 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LO residue 68 LYS Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LQ residue 42 ASP Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 286 GLN Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 37 VAL Chi-restraints excluded: chain SB residue 93 THR Chi-restraints excluded: chain SB residue 212 MET Chi-restraints excluded: chain SB residue 268 ARG Chi-restraints excluded: chain SC residue 120 ASP Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 136 VAL Chi-restraints excluded: chain SG residue 16 VAL Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SM residue 214 ASP Chi-restraints excluded: chain SR residue 381 VAL Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 1073 optimal weight: 0.1980 chunk 707 optimal weight: 0.7980 chunk 1138 optimal weight: 9.9990 chunk 695 optimal weight: 1.9990 chunk 540 optimal weight: 4.9990 chunk 791 optimal weight: 7.9990 chunk 1194 optimal weight: 7.9990 chunk 1099 optimal weight: 6.9990 chunk 951 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 734 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 177 ASN ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 67 HIS L7 184 ASN LA 75 GLN LB 77 ASN LB 188 ASN LE 127 GLN LE 131 GLN LF 44 GLN LI 65 GLN ** LK 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 21 ASN LP 121 ASN LQ 102 ASN LT 55 ASN LU 92 ASN LZ 25 GLN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 85 GLN SE 149 ASN SG 106 GLN SG 162 GLN SG 188 GLN SI 39 GLN SK 75 ASN SM 211 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN SR 595 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 159140 Z= 0.248 Angle : 0.691 19.730 232617 Z= 0.373 Chirality : 0.035 0.302 28469 Planarity : 0.007 0.134 15655 Dihedral : 22.900 179.477 68539 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.90 % Allowed : 17.20 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.09), residues: 8373 helix: 1.92 (0.09), residues: 3202 sheet: 0.40 (0.16), residues: 1080 loop : -0.17 (0.09), residues: 4091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPLW 49 HIS 0.007 0.001 HISL7 199 PHE 0.024 0.002 PHESR 376 TYR 0.023 0.002 TYRSE 102 ARG 0.017 0.000 ARGLD 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16746 Ramachandran restraints generated. 8373 Oldfield, 0 Emsley, 8373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1011 time to evaluate : 8.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 190 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8829 (mp) REVERT: L5 64 ARG cc_start: 0.8103 (ptm-80) cc_final: 0.7819 (ptm-80) REVERT: L6 8 MET cc_start: 0.8431 (mtt) cc_final: 0.8102 (mtt) REVERT: L6 69 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7933 (mptp) REVERT: L6 184 MET cc_start: 0.7977 (mtp) cc_final: 0.7282 (mtp) REVERT: LD 112 SER cc_start: 0.8132 (m) cc_final: 0.7907 (p) REVERT: LI 40 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8009 (tm-30) REVERT: LI 113 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6858 (pttm) REVERT: LJ 103 ASP cc_start: 0.7446 (t0) cc_final: 0.7166 (t70) REVERT: LK 21 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7861 (mmt90) REVERT: LL 28 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: LM 43 MET cc_start: 0.8375 (ttm) cc_final: 0.8155 (ttp) REVERT: LN 59 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: LQ 5 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7747 (mmm-85) REVERT: LT 104 MET cc_start: 0.8499 (mmt) cc_final: 0.8087 (mmt) REVERT: NL 404 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6768 (mtp-110) REVERT: SB 265 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7434 (ttt90) REVERT: SC 270 TYR cc_start: 0.8725 (t80) cc_final: 0.8434 (t80) REVERT: SD 248 ASN cc_start: 0.8074 (t0) cc_final: 0.7823 (t0) REVERT: SE 45 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8757 (mp) REVERT: SE 211 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: SG 86 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7092 (mp) REVERT: SH 156 THR cc_start: 0.7809 (p) cc_final: 0.7501 (t) REVERT: SK 67 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7501 (ptp90) REVERT: SL 94 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7276 (p0) REVERT: SM 265 TYR cc_start: 0.8358 (m-80) cc_final: 0.7985 (m-80) REVERT: SR 523 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: SR 575 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8171 (ptp-170) REVERT: SV 117 GLU cc_start: 0.6654 (tp30) cc_final: 0.6435 (tp30) outliers start: 138 outliers final: 106 residues processed: 1097 average time/residue: 2.1633 time to fit residues: 3474.4948 Evaluate side-chains 1119 residues out of total 7378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 997 time to evaluate : 7.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 129 VAL Chi-restraints excluded: chain BE residue 190 LEU Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L6 residue 190 ARG Chi-restraints excluded: chain L7 residue 153 THR Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 113 LYS Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 21 ARG Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 82 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 21 ILE Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 185 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 370 THR Chi-restraints excluded: chain LO residue 68 LYS Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 107 SER Chi-restraints excluded: chain LQ residue 5 ARG Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 20 ASN Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 29 ARG Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 33 LEU Chi-restraints excluded: chain LV residue 79 SER Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 286 GLN Chi-restraints excluded: chain NL residue 404 ARG Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 37 VAL Chi-restraints excluded: chain SB residue 93 THR Chi-restraints excluded: chain SB residue 212 MET Chi-restraints excluded: chain SB residue 265 ARG Chi-restraints excluded: chain SB residue 268 ARG Chi-restraints excluded: chain SC residue 120 ASP Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 112 GLN Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 241 VAL Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 136 VAL Chi-restraints excluded: chain SG residue 16 VAL Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 214 ASP Chi-restraints excluded: chain SR residue 381 VAL Chi-restraints excluded: chain SR residue 523 GLU Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1199 random chunks: chunk 583 optimal weight: 0.0870 chunk 755 optimal weight: 0.0050 chunk 1013 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 chunk 877 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 952 optimal weight: 1.9990 chunk 398 optimal weight: 7.9990 chunk 978 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 177 ASN ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 67 HIS L7 184 ASN LA 75 GLN LB 77 ASN LB 188 ASN LE 127 GLN LE 131 GLN LI 65 GLN ** LK 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 21 ASN LL 83 ASN LP 121 ASN LT 55 ASN LU 92 ASN LZ 25 GLN ** NP 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 85 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SG 162 GLN SG 189 GLN SI 39 GLN ** SL 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 245 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 542 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.062909 restraints weight = 347453.046| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.40 r_work: 0.2809 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 159140 Z= 0.219 Angle : 0.685 19.760 232617 Z= 0.371 Chirality : 0.034 0.300 28469 Planarity : 0.007 0.132 15655 Dihedral : 22.906 179.430 68539 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.04 % Allowed : 17.07 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.09), residues: 8373 helix: 1.91 (0.09), residues: 3203 sheet: 0.40 (0.16), residues: 1075 loop : -0.16 (0.09), residues: 4095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPSR 417 HIS 0.008 0.001 HISSL 218 PHE 0.023 0.001 PHESR 376 TYR 0.023 0.002 TYRSE 102 ARG 0.015 0.000 ARGLN 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57944.81 seconds wall clock time: 1002 minutes 3.24 seconds (60123.24 seconds total)